Table 1. Transcripts showing opposite (positive values in solid and negative in liquid or vice versa) and significant (coefficient of variation between solid and liquid cultures higher than 0.7) abundances (Fig. 4C, F, I, L, O, R, U; Fig. 5C, F, I, L).
| Function | SCO no. | Description | Log 2 (MII/MI) | SCO no. | Description | Log 2 (MII/MI) | ||
| S | L | S | L | |||||
| PRIMARY METABOLISM | SCO0992 | Cysteine synthase | −1.1 | 1.2 | SCO3909 | 50S ribosomal protein L9, rplI | −1.2 | 0.3 |
| SCO1132 | Oxidoreductase | −0.4 | 1.8 | SCO4152 | 5′-nucleotidase | 0.7 | −1.1 | |
| SCO1134 | Oxidoreductase | −1.2 | 1.9 | SCO4284 | Deacetylase | −0.5 | 1.1 | |
| SCO1181 | Putative plasmid partition protein | −2.2 | 1.2 | SCO4577 | Helicase DEAD-like | −1.2 | 1.1 | |
| SCO1335 | Oxidoreductase | −1.7 | 0.2 | SCO4701 | 30S ribosomal protein S10 | 1.2 | −1.5 | |
| SCO1343 | Uracil-DNA glycosylase | −1.2 | 0.3 | SCO4702 | 50S ribosomal protein L3 | 0.5 | −2 | |
| SCO1600 | Translation initiation factor IF-3 | 1.2 | −0.9 | SCO4703 | 50S ribosomal protein L4 | 0.4 | −2.1 | |
| SCO1631 | Helicase | −1.2 | 0.8 | SCO4712 | 50S ribosomal protein L14 | 0.7 | −1.4 | |
| SCO1966 | Excinuclease ABC subunit B | −1.9 | 0.1 | SCO4734 | 50S ribosomal protein L13 | 0.6 | −1.8 | |
| SCO2003 | DNA polymerase I | −1.8 | 0.2 | SCO5494 | NAD-dependent DNA ligase ligA | −2.2 | 0.9 | |
| SCO2036 | Tryptophan synthase subunit alpha | −0.4 | 1.4 | SCO5566 | ATP-dependent DNA helicase recG | −1.2 | 0.1 | |
| SCO2597 | 50S ribosomal protein L21 | 0.9 | −1.4 | SCO5815 | ATP-dependent DNA helicase | −1.4 | 0.7 | |
| SCO2770 | Agmatinase. Urea cycle and metabolism of amino groups | 0.4 | −1.1 | SCO5920 | DEAD-box RNA helicase | −1.7 | 0 | |
| SCO3351 | DNA repair protein RadA | −1.6 | 0.2 | SCO6084 | DNA polymerase III subunit epsilon | −2.6 | 0.8 | |
| SCO3434 | DNA polymerase I | −1 | 0.8 | SCO6262 | Helicase | −1.6 | 0 | |
| SCO3543 | Putative DNA topoisomerase I | 1.2 | −0.2 | SCO6662 | Transaldolase | −3.8 | 0 | |
| SECONDARY METABOLISM | SCO0490 | Esterase | −1.1 | 1.4 | SCO3243 | Myo-inositol phosphate synthase | −0,6 | 1.6 |
| SCO0491 | ABC transporter | −0.8 | 1 | SCO6273 | Type I polyketide synthase cpkC | −1.3 | 2.5 | |
| SCO0492 | Peptide synthetase | −1.1 | 1.2 | SCO6274 | Type I polyketide synthase cpkB | −1.9 | 3.2 | |
| SCO0493 | ABC-transporter | −1 | 1.7 | SCO6275 | Type I polyketide synthase cpkA | −1.9 | 3.2 | |
| SCO0497 | Iron-siderophore permease | −1.9 | 0.9 | SCO6276 | Secreted monooxygenase | −2.3 | 7.9 | |
| SCO0498 | Peptide monooxygenase | −2.3 | 2.7 | SCO6277 | Epoxide hydrolase | −2.3 | 6 | |
| SCO0499 | Methionyl-tRNA formyltransferase | −1.6 | 1.9 | SCO6278 | Membrane transport protein | −2 | 5.2 | |
| SCO2782 | Pyridoxal-dependent decarboxylase | −3.2 | 0.4 | SCO6279 | Aminotransferase | −1.9 | 6.4 | |
| SCO3229 | 4-hydroxyphenylpyruvic dioxygenase | −1 | 1.6 | SCO6280 | Putative transcriptional regulator | −0.7 | 4.8 | |
| SCO3235 | ABC transporter | −1 | 1.8 | SCO6281 | FAD-binding protein | −0.6 | 4.3 | |
| DIFFERENTIA-TION | SCO2705 | ChpF | 1.4 | −0.4 | SCO5112 | BldKA | 1 | −2.2 |
| SCO2607 | Sfr protein; sporulation protein | 0.6 | −1.3 | SCO5114 | BldKC | 0.6 | −2.4 | |
| SCO4069 | SarA | −0.3 | 1.6 | SCO5190 | DNA-binding protein, wblC | 3.2 | −1.6 | |
| SCO4823 | Possible target for bldA regulation | 1 | −2.8 | |||||
| REGULATORY | SCO0646 | TetR family transcriptional regulator | −1.2 | 0.1 | SCO4303 | Transcriptional regulator | −2.2 | 0.3 |
| SCO1568 | TetR family transcriptional regulator | −1.8 | 2.4 | SCO4336 | MarR-family protein | −2.6 | 0.2 | |
| SCO2489 | TetR family transcriptional regulator | −2 | 1 | SCO4375 | MarR family regulatory protein | −1.6 | 0.1 | |
| SCO2845 | GntR family transcriptional regulator | −1.3 | 0.1 | SCO4413 | AraC transcription regulator similar to S griseus AdpA | −1 | 1.9 | |
| SCO2958 | Transcriptional regulator, nnaR | −1 | 0.2 | SCO5607 | Transcriptional regulator | −0.5 | 1.8 | |
| SCO3066 | Putative regulator of Sig15 | −0.5 | 1 | SCO6267 | Putative transcriptional regulator | −1.3 | 1.8 | |
| SCO3167 | TetR family transcriptional regulator | −3.1 | 0.6 | SCO6268 | Histidine kinase | −2.4 | 2.5 | |
| SCO3275 | merR family transcriptional regulator | 0.4 | −1.2 | SCO6565 | Transcriptional regulator | −1.4 | 0 | |
| SCO3390 | Two component sensor kinase | −1.7 | 1 | SCO6694 | Transcriptional regulator | −0.9 | 2.5 | |
| SCO3696 | Transcriptional regulator | −1.1 | 0.6 | SCO6743 | Transcriptional accessory protein | −0.9 | 1.2 | |
| SCO3848 | Serine/threonine protein kinase | 1 | −0.3 | SCO7364 | TetR transcriptional regulator | −2.3 | 0.4 | |
| SCO3879 | DnaA replication initiation protein | 0.6 | −1.4 | SCO7585 | MerR transcriptional regulator | −0.6 | 2 | |
| SCO4005 | RNA polymerase sigma factor | −2.1 | 3.5 | SCO7694 | TetR transcriptional regulator | −0.8 | 1 | |
| SCO4145 | Polyphosphate kinase, ppk | −1.3 | 0.5 | |||||
| TRASPOSONS -IS | SCO7074 | Transposase | 1.4 | −0.2 | ||||
| CONJUGATION-RECOMBINATION-MUTAGENESIS | SCO5102 | MutT-like protein | −0.6 | 1.6 | SCO5770 | Recombination regulator, recX | −1.3 | 3.3 |
| SCO5769 | Recombinase A, rec A | −1.3 | 2.2 | |||||
| STRESSS - DEFENSE | SCO0774 | Cytochrome P450 | −2.9 | 1.7 | SCO3890 | Thioredoxin reductase | −1.3 | 0.1 |
| SCO0180 | Usp, universal stress protein family | −1.1 | 1.5 | SCO4761 | Co-chaperonin GroES | −1.8 | 1.5 | |
| SCO3669 | Chaperone protein DnaJ | −0.5 | 1.6 | SCO4762 | GroEL1 | −1.4 | 0.5 | |
| SCO3670 | Heat shock protein GrpE | −0.8 | 1.6 | SCO5254 | SodN, superoxide dismutase | −1.2 | 1.3 | |
| SCO3701 | Putative thioredoxin reductase | −1.7 | 0.6 | |||||
| CATABOLISM -DEGRADATION | SCO3000 | Phosphatase | −1.2 | 1.2 | SCO4798 | Peptidase | 1.1 | −0.5 |
| SCO3487 | Agarase | 3.8 | −1 | SCO5285 | ATP-dependent protease | −1.3 | 3.6 | |
| SCO3661 | ATP-dependent protease, clpB | −2.1 | 0.7 | SCO5446 | Probable zinc metalloprotease | 1.6 | 0 | |
| SCO3712 | Hydrolase | −1.9 | 1.1 | SCO6109 | Probable secreted hydrolase | −1.4 | 0.1 | |
| SCO4241 | Proteinase | 1.2 | −0.3 | SCO7263 | Chitinase | 1.2 | −0.2 | |
| TRANSPORTERS - SECRETED | SCO0119 | Possible small secreted protein | 1 | −0.3 | SCO3607 | Secreted protein | −4.1 | 0.1 |
| SCO0994 | Putative transport permease protein | −0.7 | 2 | SCO4243 | Putative secreted protein | 0.7 | −1.5 | |
| SCO0286 | Putative peptidoglycan binding protein | 0.5 | −2.8 | SCO4289 | Possible secreted protein | −1.9 | 0.1 | |
| SCO1292 | Putative secreted protein | −1.6 | 1.3 | SCO4585 | ABC transporter protein | −0.3 | 2.4 | |
| SCO1515 | Preprotein translocase subunit SecF | 0.4 | −1.2 | SCO4722 | Preprotein translocase SecY | 0.5 | −1.5 | |
| SCO1516 | Preprotein translocase subunit SecD | 0.5 | −1.5 | SCO4993 | Metal ion transport protein | 0.8 | −1.1 | |
| SCO1567 | Transmembrane-transport protein pqrB | −1.4 | 2.3 | SCO5016 | Possible secreted protein | 1.1 | −0.3 | |
| SCO1785 | Iron-siderophore | −1.3 | 0.1 | SCO5130 | ABC transporter | 0.6 | −1.3 | |
| SCO2074 | Lipoprotein signal peptidase | 0.7 | −1.3 | SCO6199 | Possible secreted esterase | −1.3 | 2.1 | |
| SCO2949 | Carboxyvinyltransferase, murA | 0.5 | −1.2 | SCO6272 | Possible secreted protein | −1.9 | 1.9 | |
| SCO3024 | Transport protein | 0.5 | −1.3 | SCO6320 | Transport membrane protein | −1.1 | 0.1 | |
| SCO3166 | Membrane transport protein | −2.3 | 0.6 | SCO6665 | Probable secreted glucosidase | 0.4 | −1 | |
| SCO3286 | Putative secreted protin | −3.1 | 0.5 | SCO6980 | ABC transporter membrane protein | 1.4 | 0 | |
| SCO3366 | Exporter | −1.8 | 0.4 | SCO7453 | Putative secreted protein | 3.4 | −0.6 | |
Average log2 abundance values from three biological replicates of the MII with respect to MI in solid (S) and liquid (L) cultures. Only transcripts with significant abundances are shown (log2 abundance greater than ±1 in liquid and/or solid cultures). Functions (according to Gene bank, Gene Ontology, Conserved Domain, and KEGG and StrepDB databases): Primary metabolism (DNA/RNA replication, aerobic and anaerobic energy production, glycolysis and glyconeogenesis, pentose phosphate pathway, amino acid metabolism, nucleotide metabolism, translation, protein folding, RNA/protein processing, nucleases/RM methylases); secondary metabolism (secondary metabolites synthesis); differentiation (TTA bldA targets, Bld and Whi proteins); regulatory genes (transcriptional regulators, kinases, other regulatory genes); transposons - insertion sequences; conjugation – recombination - mutagenesis; stress and defense proteins; catabolism - degradation; lipid metabolism; transporters and secreted (ABC transporters, transporters and secreted proteins). Genes with “unknown” functions (Table S1) were not included.